|MadSci Network: Astronomy|
The basic reason is simple - shadows! The moon is not a flat sphere; instead, it has craters, valleys, and mountains created by meteor impacts. These mountains, craters, and hills cast shadows across the moon's surface in exactly the same way hills cast shadows when the sun is hitting them here on earth. Many of the dark spots you see are simply craters - they are deep enough below the surface to be immersed in shadow.
I would recommend getting a look at the moon with binoculars or a telescope if you can - then the craters become very clear and you can see exactly what is going on.
Try the links in the MadSci Library for more information on Astronomy.